rs782339253

Variant names:

• chr1-145961000-C-G
• rs782339253
• NM_001039888.4:c.760G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-145961000-C-G
• chr1-145961000-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001039888.4(ANKRD34A):​c.760G>C​(p.Ala254Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A254T) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: ANKRD34A NM_001039888.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.61
• Publications: 0 publications found

Genes affected

ANKRD34A (HGNC:27639): (ankyrin repeat domain 34A)

ENSG00000280778 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039888.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD34A	NM_001039888.4	MANE Select	c.760G>C	p.Ala254Pro	missense	Exon 4 of 4	NP_001034977.1	Q69YU3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD34A	ENST00000606888.3	TSL:2 MANE Select	c.760G>C	p.Ala254Pro	missense	Exon 4 of 4	ENSP00000475189.1	Q69YU3
	ENSG00000280778	ENST00000625258.1	TSL:5	c.-29-16084C>G		intron	N/A	ENSP00000487094.1	A0A0D9SG24
	ANKRD34A	ENST00000855736.1		c.760G>C	p.Ala254Pro	missense	Exon 2 of 2	ENSP00000525795.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_noAF	Uncertain	0.12
CADD	Pathogenic	28
DANN	Uncertain	0.99
DEOGEN2	Benign	0.038	T
LIST_S2	Benign	0.76	T
MetaRNN	Uncertain	0.63	D
PhyloP100		7.6
Sift4G	Uncertain	0.051	T
Vest4		0.61
gMVP		0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs782339253; hg19: chr1-145474088;